From 426c73f671441028a570958cc8ea48d85a0a2b16 Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Fri, 5 Jul 2024 13:34:12 +0200 Subject: [PATCH 1/5] Readme update. --- README.md | 32 ++++++++++++++++++++++++++++---- 1 file changed, 28 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index f6710395..996c6e8f 100644 --- a/README.md +++ b/README.md @@ -34,19 +34,43 @@ The full list of capabilities and features is listed in the [project documentati The released versions of `yadg` are available on the Python Package Index (PyPI) under [yadg](https://pypi.org/project/yadg). Those can be installed using: ```bash - pip install yadg +pip install yadg ``` If you wish to install the current development version as an editable installation, check out the `master` branch using git, and install `yadg` as an editable package using pip: ```bash - git clone git@github.com:dgbowl/yadg.git - cd yadg - pip install -e . +git clone git@github.com:dgbowl/yadg.git +cd yadg +pip install -e . ``` Additional targets `yadg[testing]` and `yadg[docs]` are available and can be specified in the above commands, if testing and/or documentation capabilities are required. +### Usage: +After installing `yadg`, you can extract data from single files of known filetypes using: + +```bash +yadg extract [outfile] +``` + +This will write the data extracted from the `infile` into a NetCDF file called `outfile`. An example usage for BioLogic MPR files would be: + +```bash +yadg extract eclab.mpr example_file.mpr output_file.nc +``` + +Alternatively, you can obtain a `DataTree` object in Python via: + +```python +import yadg +yadg.extractors.extract(filetype=, path=) +``` + +More detailed [usage instructions](https://dgbowl.github.io/yadg/master/usage.html) are available in the project documentation. + + + ### Contributors: - [Peter Kraus](http://github.com/PeterKraus) - [Nicolas Vetsch](http://github.com/vetschn) From a73f73e5d3b05b5d152c916b67958f5a63d78ffb Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Fri, 5 Jul 2024 13:35:25 +0200 Subject: [PATCH 2/5] Fix date in 5.1 release docs. --- docs/source/version.5_1.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/version.5_1.rst b/docs/source/version.5_1.rst index 9ae45ace..ecc5b7ed 100644 --- a/docs/source/version.5_1.rst +++ b/docs/source/version.5_1.rst @@ -4,7 +4,7 @@ :target: https://github.com/PeterKraus/yadg/tree/5.1 .. image:: https://img.shields.io/static/v1?label=yadg&message=v5.1&color=blue&logo=pypi :target: https://pypi.org/project/yadg/5.1/ -.. image:: https://img.shields.io/static/v1?label=release%20date&message=2024-XX-YY&color=red&logo=pypi +.. image:: https://img.shields.io/static/v1?label=release%20date&message=2024-07-01&color=red&logo=pypi Developed in the |concat_lab|_ at Technische Universität Berlin (Berlin, DE). From 20de1e98987b8562090992f5a232cf41847157f4 Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Fri, 5 Jul 2024 13:40:07 +0200 Subject: [PATCH 3/5] More minor readme touches. --- README.md | 4 ---- 1 file changed, 4 deletions(-) diff --git a/README.md b/README.md index 996c6e8f..33e6e799 100644 --- a/README.md +++ b/README.md @@ -27,7 +27,6 @@ Additionally, data from multiple files of the same type, or even of different ty - original metadata from the extracted files is stored under `original_metadata` - extensive *dataschema* validation using provided specifications - The full list of capabilities and features is listed in the [project documentation](http://dgbowl.github.io/yadg). ### Installation: @@ -69,14 +68,11 @@ yadg.extractors.extract(filetype=, path=) More detailed [usage instructions](https://dgbowl.github.io/yadg/master/usage.html) are available in the project documentation. - - ### Contributors: - [Peter Kraus](http://github.com/PeterKraus) - [Nicolas Vetsch](http://github.com/vetschn) ### Acknowledgements - This project has received funding from the following sources: - European Union’s Horizon 2020 programme under grant agreement No 957189. From c0085e675cce63283d1336418abd71c8fa0b401d Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Fri, 5 Jul 2024 13:45:35 +0200 Subject: [PATCH 4/5] CI master -> main --- .github/workflows/lint-every-pr.yml | 2 +- .github/workflows/pull-request-commit.yml | 2 +- .github/workflows/{push-master.yml => push-main.yml} | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) rename .github/workflows/{push-master.yml => push-main.yml} (95%) diff --git a/.github/workflows/lint-every-pr.yml b/.github/workflows/lint-every-pr.yml index 52a927a2..efb579d9 100644 --- a/.github/workflows/lint-every-pr.yml +++ b/.github/workflows/lint-every-pr.yml @@ -2,7 +2,7 @@ name: lint-every-pr on: pull_request: branches: - - master + - main jobs: lint: runs-on: ubuntu-latest diff --git a/.github/workflows/pull-request-commit.yml b/.github/workflows/pull-request-commit.yml index f3387db9..3a05f98b 100644 --- a/.github/workflows/pull-request-commit.yml +++ b/.github/workflows/pull-request-commit.yml @@ -1,7 +1,7 @@ name: pull-request-commit on: pull_request: - branches: ['master'] + branches: ['main'] jobs: build: strategy: diff --git a/.github/workflows/push-master.yml b/.github/workflows/push-main.yml similarity index 95% rename from .github/workflows/push-master.yml rename to .github/workflows/push-main.yml index 51bbb74a..19db99bf 100644 --- a/.github/workflows/push-master.yml +++ b/.github/workflows/push-main.yml @@ -1,7 +1,7 @@ -name: push-master +name: push-main on: push: - branches: ['master'] + branches: ['main'] jobs: build: uses: ./.github/workflows/workflow-build.yml From c886371ff18feab49ee5bc02cf8588432da6a759 Mon Sep 17 00:00:00 2001 From: Peter Kraus Date: Fri, 5 Jul 2024 13:47:08 +0200 Subject: [PATCH 5/5] more master -> main --- .github/workflows/push-main.yml | 2 +- .github/workflows/workflow-pages.yml | 4 ++-- README.md | 6 +++--- pyproject.toml | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/.github/workflows/push-main.yml b/.github/workflows/push-main.yml index 19db99bf..c97040e3 100644 --- a/.github/workflows/push-main.yml +++ b/.github/workflows/push-main.yml @@ -31,7 +31,7 @@ jobs: - uses: actions/download-artifact@v4 with: name: public-ubuntu-latest-3.9 - path: public/master + path: public/main - uses: peaceiris/actions-gh-pages@v3 with: github_token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/workflow-pages.yml b/.github/workflows/workflow-pages.yml index a926c8ac..bbcf10fd 100644 --- a/.github/workflows/workflow-pages.yml +++ b/.github/workflows/workflow-pages.yml @@ -32,8 +32,8 @@ jobs: shell: bash run: | sphinx-apidoc -o docs/source/apidoc src/yadg -T -M -f --templatedir=docs/apidoc_t - sphinx-build -W -b html docs/source public/master + sphinx-build -W -b html docs/source public/main - uses: actions/upload-artifact@v4 with: name: public-${{ inputs.os }}-${{ inputs.pyver }} - path: public/master + path: public/main diff --git a/README.md b/README.md index 33e6e799..479e27ac 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ [![Documentation](https://badgen.net/badge/docs/dgbowl.github.io/grey?icon=firefox)](https://dgbowl.github.io/yadg) [![PyPi version](https://badgen.net/pypi/v/yadg/?icon=pypi)](https://pypi.org/project/yadg) [![Github link](https://badgen.net/github/tag/dgbowl/yadg/?icon=github)](https://github.com/dgbowl/yadg/) -[![Github status](https://badgen.net/github/checks/dgbowl/yadg/?icon=github)](https://github.com/dgbowl/yadg/actions/workflows/push-master.yml) +[![Github status](https://badgen.net/github/checks/dgbowl/yadg/?icon=github)](https://github.com/dgbowl/yadg/actions/workflows/push-main.yml) # ![yet another datagram](./docs/source/images/yadg_banner.png) @@ -36,7 +36,7 @@ The released versions of `yadg` are available on the Python Package Index (PyPI) pip install yadg ``` -If you wish to install the current development version as an editable installation, check out the `master` branch using git, and install `yadg` as an editable package using pip: +If you wish to install the current development version as an editable installation, check out the `main` branch using git, and install `yadg` as an editable package using pip: ```bash git clone git@github.com:dgbowl/yadg.git @@ -66,7 +66,7 @@ import yadg yadg.extractors.extract(filetype=, path=) ``` -More detailed [usage instructions](https://dgbowl.github.io/yadg/master/usage.html) are available in the project documentation. +More detailed [usage instructions](https://dgbowl.github.io/yadg/main/usage.html) are available in the project documentation. ### Contributors: - [Peter Kraus](http://github.com/PeterKraus) diff --git a/pyproject.toml b/pyproject.toml index 482f5f3b..6d24c8f0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -51,7 +51,7 @@ docs = [ ] [project.urls] -Documentation = "https://dgbowl.github.io/yadg/master" +Documentation = "https://dgbowl.github.io/yadg/main" Issues = "https://github.com/dgbowl/yadg/issues" Repository = "https://github.com/dgbowl/yadg/"